Well i encounter the issue in many films. For example Dark night (some scenes are in full screen some not) 1080p mkv, Quantum of solace 1080p mkv and many other. Is there a way to transcode them in 16:9 or not? I'm realy dissapointed (not from this amazing software) because i bought recently a 46inch HDTV and i cannot see my films in full screen

Most movie lovers dont want to mess with the directors original vision so personally I wouldnt cut away parts of the original picture just to fill the screen (or even worse, stretch it),that is almost going back to 4:3 TV's again. Almost all movies made for cinema is made in an aspect ratio greater than 16:9 (1,78) so black bars will be present from all sorts of sources (bluray, cable, sat.. whatever).

(only reason parts of the Dark Knight sometimes has 16:9 format is because some scenes were shot with IMAX equipment.)

But what you want is probably possible by reading the manual to "mplayer/mencoder" and playing with the "mencoder" options in the transcoding setting. But in my (not so humble ) opinion that is too much trouble and only depraves you of seeing the movie in the way it was meant to be seen...